1ZNV

How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal ion cofactor

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d1znvc_	All alpha proteins	Acyl carrier protein-like	Colicin E immunity proteins	Colicin E immunity proteins	ImmE7 protein (Im7)	(Escherichia coli str. K-12 substr. W3110 ) [TaxId: 316407 ],	SCOPe (2.08)
A	d1znva_	All alpha proteins	Acyl carrier protein-like	Colicin E immunity proteins	Colicin E immunity proteins	ImmE7 protein (Im7)	(Escherichia coli str. K-12 substr. W3110 ) [TaxId: 316407 ],	SCOPe (2.08)
B	d1znvb_	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	HNH-motif	DNase domain of colicin E7	(Escherichia coli str. K-12 substr. W3110 ) [TaxId: 316407 ],	SCOPe (2.08)
D	d1znvd_	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	HNH-motif	DNase domain of colicin E7	(Escherichia coli str. K-12 substr. W3110 ) [TaxId: 316407 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Colicin E immunity proteins	8037162	3001814	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Colicin E immunity proteins	8037162	3001814	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	His-Me finger endonucleases	8043906	3001893	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	His-Me finger endonucleases	8043906	3001893	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Colicin_Pyocin	e1znvC1	A: alpha bundles	X: ACP-like	H: Colicin E immunity proteins (From Topology)	T: Colicin E immunity proteins	F: Colicin_Pyocin	ECOD (1.6)
A	Colicin_Pyocin	e1znvA1	A: alpha bundles	X: ACP-like	H: Colicin E immunity proteins (From Topology)	T: Colicin E immunity proteins	F: Colicin_Pyocin	ECOD (1.6)
B	LHH	e1znvB1	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: LHH	ECOD (1.6)
D	LHH	e1znvD1	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: LHH	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.10.1200.20	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
A	1.10.1200.20	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
B	3.90.540.10	Alpha Beta	Alpha-Beta Complex	Colicin E7 immunity protein	Chain B, fragment: Endonuclease domain	CATH (4.3.0)
D	3.90.540.10	Alpha Beta	Alpha-Beta Complex	Colicin E7 immunity protein	Chain B, fragment: Endonuclease domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF01320	Colicin immunity protein / pyocin immunity protein (Colicin_Pyocin)	Colicin immunity protein / pyocin immunity protein	-	Domain
B, D	PF21431	Colicin/Pyocin-S2, DNase domain (Col-Pyo_DNase)	Colicin/Pyocin-S2, DNase domain	This entry represents the DNAse domain from colicin/pyocin bacteriocins, such as pyocin-S2 from Pseudomonas aeruginosa and colicin E7/E9 from E. coli. This domain has an alpha/beta fold containing a Zn2+ ion binding site [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Colicin E7 immunity protein	binding toxic substance binding	cellular metabolic process metabolic process cellular process bacteriocin immunity toxin metabolic process secondary metabolic process	-
B, D	Colicin E7	endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus cellular process disruption of cell in another organism disruption of anatomical structure in another organism biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing	intracellular anatomical structure extrachromosomal circular DNA cellular anatomical entity extrachromosomal DNA

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR000290	Colicin immunity protein/pyocin immunity protein	Family
A, C	IPR035900	Colicin E immunity protein superfamily	Homologous Superfamily
B, D	IPR024575	Cloacin/colicin	Family
B, D	IPR024566	Colicin, receptor domain	Domain
B, D	IPR016128	Pyosin/cloacin translocation domain	Domain
B, D	IPR036302	Pyosin/cloacin translocation domain superfamily	Homologous Superfamily
B, D	IPR037146	Colicin/pyocin, DNase domain superfamily	Homologous Superfamily
B, D	IPR044925	His-Me finger superfamily	Homologous Superfamily
B, D	IPR003615	HNH nuclease	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
B	Colicin-E7 M-CSA #838	The ColE7 endonuclease from Escherichia coli binds nucleic acids and hydrolyses a phosphodiester bond. It contains the His-metal finger motif and may function with a range of metals, although the physiological metal is thought to be Zn(II).	Defined by 5 residues: ARG:B-5 [auth B-447]HIS:B-102 [auth B-544]GLU:B-103 [auth B-545]HIS:B-127 [auth B-569]HIS:B-131 [auth B-573] Some residues are not modelled and lack atomic coordinates. Visualization is not available. Some residues are not modelled and lack atomic coordinates. Structure Motif searching is not available. EC: 3.1 (PDB Primary Data)

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.